One of the things you can do is set up Acrobat to process a folder and use "Generic application" in Switch to drop files into that folder and pick them up in the output folder.
If you only want to run Javascripts you can also do that with the Acrobat Configurator.
What is it you want to do with the PDF file? There are other tools out there like the ones from Apago that can do nice things with PDF files without requiring the file to be opened in Acrobat.
Freddy